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MetaSUB / metasub_utils

MIT License
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how can i solve this metasub_utils.pangea.cli #14

Open wnvcks opened 3 years ago

wnvcks commented 3 years ago

Description

Hi. my name is Juchan.hwang pasteur institut when i tried to find Seoul_COVID19 data. i cannot find recent data project name : haib20CEM6134 i only can see the list of project haib18CEM5453

and also when i did other command

What I Did

root@juchan-VirtualBox:~/Desktop# metasub wasabi list nonhuman-reads --city-name seoul > all_seoul_sample_list.txt
Unable to import metasub_utils.pangea.cli

root@juchan-VirtualBox:~/Desktop# 

this is the some result of list that i command. i cannot see the project haib20CEM6134 about Seoul_COVID19 result 

s3://metasub/human_filtered_data/hudson_alpha_library/haib18CEM5453/HNHKFCCXY/haib18CEM5453_HNHKFCCXY_SL345999.filter_human_dna.nonhuman_read1.fastq.gz
s3://metasub/human_filtered_data/hudson_alpha_library/haib18CEM5453/HNHKFCCXY/haib18CEM5453_HNHKFCCXY_SL345999.filter_human_dna.nonhuman_read2.fastq.gz
s3://metasub/human_filtered_data/hudson_alpha_library/haib18CEM5453/HNHKFCCXY/haib18CEM5453_HNHKFCCXY_SL346000.filter_human_dna.nonhuman_read1.fastq.gz
s3://metasub/human_filtered_data/hudson_alpha_library/haib18CEM5453/HNHKFCCXY/haib18CEM5453_HNHKFCCXY_SL346000.filter_human_dna.nonhuman_read2.fastq.gz
s3://metasub/human_filtered_data/hudson_alpha_library/haib18CEM5453/HNHKFCCXY/haib18CEM5453_HNHKFCCXY_SL346001.filter_human_dna.nonhuman_read1.fastq.gz
dcdanko commented 3 years ago

Thank you for the detailed issue, this interface is actually deprecated (though my bad for not making that clear). To download MetaSUB data you should use the Pangea API. Hopefully the info below gets you up and running if not please keep replying to this thread.

You can find directions to use the API here https://pangeabio.io/docs/how-to-download-data The data for Seoul is here https://pangeabio.io/sample-groups/7a01ea3e-df47-4a04-94f8-969ecf5ae2b6

Ultimately the command you'll need to run is

pangea-api download sample-results --module-name "cap2::clean_reads" "MetaSUB Consortium" "MetaSUB Seoul"

This will download files one at a time. You may want to include the --urls-only flag with the above command to get a list of urls instead which you can download with wget or similar.

tiana-yuchen commented 1 year ago

Hi. Thanks for your amazing work!! but I find that I could not access Pangea to register or browse the organization/data repo. It always appears "Error Cannot destructure property 'status' of 'error.response' as it is undefined." Is it because it has suspended? Thanks!